CA1292606C

CA1292606C - Continuous flow reactor for sequencing peptide sequenators

Info

Publication number: CA1292606C
Application number: CA000543487A
Authority: CA
Inventors: John E. Shively
Original assignee: Beckman Research Institute of City of Hope
Current assignee: Beckman Research Institute of City of Hope
Priority date: 1986-08-15
Filing date: 1987-07-30
Publication date: 1991-12-03
Anticipated expiration: 2008-12-03
Also published as: EP0256676A3; DE3750624T2; EP0256676B1; DE3750624D1; NZ221441A; EP0256676A2; AU7634387A; JPS63184065A; AU618515B2

Abstract

ABSTRACT
A continuous flow reactor for a peptide sequenator, the continuous flow reactor being assembled by interference fit joints from a plurality of tubes of pliable, chemically inert material such as polytetrafluoroethylene. One tube section is packed, e.g., with silica beads coated with the peptide to be sequenced and is provided with inlet and outlet tubes for attachment to a sequenator.

Description

i~2t~06 ~ITLE

.A CONTINUOUS FLOW REACTOR FOR
lSEQ~ENCING PEPTIDE SEQUENATORS

I ~ackground of the Invention 1~
A. Field of the Invention This invention relates to apparatus and methods for peptide sequencing. In particular, the invention relates to a continuous flow column reactor for a peptide sequenator and to a peptide sequencing method in which the reactor is utilized.

B. Descri~tion of the Prior Art Practical automated peptide sequencing dates from the 1967 introduction of the spinning cup sequenator. See Edman, P., and Begg, G., A Protein Sequenator, European Journal of BiochemistrY, 1, 80-91 (1967). A focal problem associated with the spinning cup sequenator is sample loss, particularly of short peptides.
Therefore, an alternative method - solid phase degradation--was designed whereby reagents and solvents are passed in an appropriate program through a column packed with a solid support such as a polystyrene matrix or preferably glass beads to which a peptide is covalently attached. Both the column and the tubing by wheich it is connected to the sequenator may be formed from polytetrafluoroethylene, e.g., Teflon. See Laursen, R.A., A
Solid-Phase Peptide Sequenator, European Journal of Biochemistry,¦
20, 89-102 (1971) and Shively, "Methods of Protein Mischaracterization," Humana Press, Clifton, N. J. (1986), Chapter 9.
In 1981, a sequenator that employs gas phase reagents instead of liquid phase reagents at critical points in the Edman degradation was proposed. See Hewick, R.M., Hunkapillar, M.W., !

Hood, L.E., Dreyer, W.J., A Gas-Liquid Solid Phase Peptide and Protein Sequenator, T~e Jour~l of Bioloaical Chemistry, 25~, 7990-7997 (1981) and Shively, supra, Chapter 8, Sec. 314, p.229. This device includes a two-part glass cartridge assembly which houses a miniaturecontinuous flow glass reaction chamber in which the peptide sample is presented as a dispersion in a thin film of a Polybrene supported on a porous glass fiber disk. Means are provided for disconnecting the cartridge from its mounting base each time the sample is loaded. The cartridge is vertically mounted in a sequenator to which it is connected at its inlet and outlet ends by Teflon tubing.
A modification of the Hewick, et al. sequenator is described by Hawke, Harris and Shively in AnalYtical Biochemistrv, 147, 315-330 (1985), and Shively, suPra, Chapter 7, page 210, et seq. This modification replaces the glass reactor cartridge assembly of Hewick, et al.
with an all Teflon cartridge of similar design, thus providing an all Teflon delivery and reaction system. The sample is presented within the reaction chamber on a trimethylsilyated glass fiber disk. Hawke, et al., noting that Teflon is "self-sealing", report lower background levels deemed to be consequent from a better seal achieved in the all Teflon design as compared to the seal observed with the Hewick, et al. glass cartridge. The all Teflon design of the instrument is also reported to be responsible for increased yields. See Shively, su~ra, at p.217.
Design of a multipurpose sequenator is discussed in Shively, supra, in Chapter 9, page 249, et seq. Such a multipurpose machine is constructed in units which are interchangeable so that it may be easily converted to run with a cup compartment, a column, or a cartridqe. In the discussion of "Exchangeable Parts", it is explained the micro columns adapted for microsequencing is solid phase sequenators can be replaced by a ~r G()6 cartridge without changin~ the other parts of the apparatus. A
polyfluorochloro (Xel-F) micro column filled with peptide bound glass support and provided with Teflon tubing inlet and outlet lines for attachment to a sequenator is described.

Summarv of the Invention This invention provides a continuous flow column reactor substantially free of unswept volumes in which accumulation of amino acids, by products and reagents is substantially eliminated. The reactor is inexpensive and is easily inserted into and removed from the sequenator, thus facilitating the frequent use of new and uncontaminated chambers.
The reactor of the invention is formed from chemically inert synthetic resin tubing. A reaction chamber formed from a sectio~
of such tubing of relatively large internal diameter is provided with interference fitted inlet and outlet tubes of appropriate dimension. ~n the preferred embodiment of the invention, the reactor is form.ed from "Teflon" (trade mark) tubing. The reaction chamber is provided with a porous support member, preferably Teflon, and packed with discrete articles, e.g., glass beads, coated with th~
peptide to be seguenced.

An aspect of the invention is as follows:

_ 3 1~2606 A continuous flow reactor including a first tube for passing reactive fluids and solvents from a peptide sequenator into a reaction chamber packed with peptide coated discrete objects and a second tube for removal of solvents and reaction products from the reaction chamber which comprises:
(A) a reaction chamber formed from a pliable, chemically inert tube;
(B~ first and second pliable, chemically inert tubes for connecting the reaction chamber to a sequenator, (C) the inside and outside diameters of said reaction chamber tube and said first and second connecting tubes being so dimensioned that two leak-tight interference fit joints are provided by i~serting one end section of a tube into the end section of another tube, one of said leak-tight interference fit joints being provided between said first tube and said reaction chamber and the other being provided between said second tube and said reaction chamber.

~rief Descri~tion of the Drawinqs The novel features of the invention will be more readily appreciated from the following description when read in conjunction with the appended drawings, in which corresponding components are designated by the same reference numerals throughout the various figures.
l Figure 1 is an elevational view, in section, of a continuous : flow reactor constituting one embodiment of the invention;

Figure 2 is a sectional view, in plan, of a discrete object with one coating used in the continuous flow reactor shown in Figure 1;
Figure 3 is a sectional view, in plan, of a discrete object, e~g., glass bead, with two coatings used in the continuous flow reactor shown in Figure l;
Figure 4 is an elevational view, in section, of a continuous flow reactor constituting an alternative embodiment of the invention; and Figure 5 is a comparative set of chromatograms obtained using a continuous flow reactor of the present invention and a prior art cartridge reactor chamber.

Detailed Description of the Invention A continuous flow reactor according to the present invention is shown in Figure l where it is generally designated by reference numeral 10. The continuous flow reactor 10 includes reaction tube 14 and interference fitted supply and drain tubes 12 and 16. Each of the tubes 12, 14 and 16 is formed from chemically inert, pliable synthetic resinous material, preferably a self-lubricating fluorocarbon such as a polytetrafluoro-ethylene. Numerous fluorocarbons are available. See, e.g., Plastics Enaineerinq Handbook, Van Nostrand Reinhold Co. (1976), pp. 60-62.
Each of the tubes 12 and 16 may be of substantially the same size, and the reaction tube 14 may be larger than the tubes 12 and 16. For example, the tubes 12 and 16 may have an outer diameter of approximately one-sixteenth of an inch (1/16") and the reaction tube 14 may have an inner diameter of approximately one-sixteenth of an inch (1/16") and an outer diameter of approximately one-eighth of an inch (118"). Preferably, the inner diameter of the reaction tube 14 is slightly undersized X

1;~9'Z~06 relative to the outer diameters of the tubes 12 and 16. With these size relationships, the tubes 12 and 16 can be interferenc or press fitted into the opposite ends of the reaction tube 14 t provide leak-tight joints between the tubes 12 and 16 and the reaction tube 14.
Alternatively, the tube 16 may be larger and so dimensioned as to provide a press fit on the outside instead of the inside of the reaction tube 14 as shown in Figure 1. A reaction zone free of unswept volumes is provided in this manner.
A porous support member 18, such as a disk, is tightly fitted inside the reaction tube 14. Preferably, the support member 18 is positioned near the location of the upper edge of the tube 16 in the embodiment shown in Figure 1. The support member 18 has a porosity requisite to allow passage of fluids and yet retain discrete objects 20, such as beads packed into the upper portion of the reaction tube 14. Support member 18 is formed from a chemically inert synthetic resin, preferably a fluorocarbon. For example, the support member 18 may be made from polytetrafluoroethylene cut by a 14-gauge needle to provide a circular disk slightly larger than the inner diameter of the reaction tube 14. The disk can be pressed into the reaction tube 14 where it will be retained in the desired position by the resulting press fit.
Useful support members 18 may be formed from a synthetic resinous material sold under the trademark "ZITEX~. This material is available from a number of suppliers including Norton¦
Chemplast, 150 Dey Road, Wayne, New Jersey in different porosities such as extra fine, fine and medium. Materials with all of these different porosities can be used satisfactorily in the continuous flow reactor 10 constituting this invention.

The reaction tube 14 is appropriately packed with discrete objects 20. Preferably, the discrete objects are made from a l ll ! _ 5 _ Zti06 material such as a porous silica. The discrete objects 20 may be irregular or spherical. Suitable discrete ob~ects 20 having an lrregular and porous con~iguration may be obtained from Electro-Nucleonics, 368 Passaic Avenue, Fairfield, New Jersey. Preferred irregular discrete objects 20 have a mesh size between one hundred and twenty (120) and two hundred (200) and a pore size of approximately three hundred and seventy nine angstroms (379 A). Silica packing material meeting these specifications are available as GC Porasils B
and C from Waters Chromatography Division of Millipore Corporation, 34 Maple Street, Milford, Massachusetts. See Waters Sourcebook for Chromato~ra~hv Columns and Su~lies (1986).
Spherical discrete objects 20 having a diameter of from about one hundred microns (100~) to three hundred microns (300~) are preferred. Each spherical object when packed in the reaction chamber 14 provides spacings which assure that fluids will flow along substantially non-linear paths and will be drained without entrapment. The provision of non-linear flow paths is further facilitated by the use ofpackings which comprise a plurality of different sized spherical objects. For example, a mixture of spherical particles of different diameters in the range of one hundred microns (100~) to three hundred microns (300~) is appropriate.
Silica derivatives, such as octadecyl silica and octyl silica, may also be used for the discrete objects 20 and may be preferred for the sequencing of certain peptides or proteins. Various other silica derivatives currently available for reverse phase high performance liquid chromatography may be used. Such derivatives may be either specifically prepared for use in the reactor of this invention, manufactured or purchased. Waters GC Porasils B
and C and Waters GC Bondapack C18 material have been 1~2606 used as a starting material for the preparation of silica derivatives.
The discrete objects 20 can be coated with a peptide 22 (se Figure 2) which is to be seguenced. For example, one microgram of the peptide 22 may be provided for each milligram of the discrete objects 20. In a specific case, 1-3 micrograms of sper whale apomyoglobin have been added to 5-10 milligrams of the discrete o~jects 20.
The minimum amount of sample depends on the purity, molecular size and the desired number of amino acid residues to be determined and can be as low as 0.1 to 10 picomoles. 10 to 2 milligrams of discrete objects 20 is frequently adequate to retain sample amounts in the range of 0.1 to 10,000 picomoles.
However, the reguired quantity of such objects may vary by as much as much as tenfold for certain applications.
Alternatively, a first coating material 24 (see Figure 3), such as Polybrene which has affinity both for the objects and th peptides, may be coated on the discrete objects 20 before the peptide 22 is applied. A Polybrene coating is particularly appropriate when porous discrete objects are utilized.
Preferably, at least one milligram of Polybrene per milligram of discrete objects 20 is applied. However, the amount of Polybren~
may vary above or below this amount by approximately fifty percent (50%).
When Polybrene is applied to 5-lO mg of the discrete objectc 20 which are packed in the reaction tube 14 with a length of 3 c~
and a particle bed of 0.5-1.0 cm (5-10 mg of silica), an amount ¦
of approximately five microliters (5 1) of 100 mg/ml Polybrene may be applied to the reaction tube 14 so there is an adequate filling with the discrete objects 20 to a height of approximatel~

0.5-1.0 cm. When applied to the discrete objects 20 on a bulk basis outside of the reaction tube 14, a volume of 100 mg/ml _ 7 _ l~:~Z~06 Polybrene sufficient to wet the discrete objects 20 over their complete surfa~es is applied. For 10 mg of silica, a solution o approximately 300 mg/ml of Polybrene may be employed. The discrete objects 20 may then be dried in a vacuum desicator.
In an alternative embodiment of the invention, a closure member 26 (see Figure 4) is disposed in the reaction tube 14 at c position near the end of the tube 12. The closure member 26 may be constructed in a manner similar to that for the support membe~
18. The closure member 26 encloses the top of the reaction tube 14 to confine the discxete objects 20.
The continuous flow reactor 10 is connected by the tube 12 to an apparatus (sequenator) for introducing reactive fluids, e.g., Edman reagents, for N-terminal sequencing, or Stark reagents for C-terminal sequencing.
The continuous flow reactor 10 described above has certain important advantages. These include the following:
(1) It is inexpensive, disposable, simple to construct, and easy to install into and remove from a sequenator. These features permit a series of reactors to be precharged and subsequently inserted into the sequenator as needed.

(2) It has little unswept volume, i.e., volumes not flushed with fluids, where materials can accumulate. Substantially, leakproof seals to vapors and fluids are provided throughout the length of the reactor. These features minimize the accumulation of by-products or successive amino acids isolated from the sequenced peptide and, hence, the background which may interfere with the chromatogram identification of successive amino acids from the peptides.

(3) It has few, if any, surfaces at which amino acids or by-products can be entrapped and accumulated which would later leach ba into the flow stream and generate backgro~nd signals t~06 in successive isolations of amino ac$d derivatives from a peptide.

(4) The discrete objects 20 disposed in the reaction tube 14 can be used as a sample concentrator in a method similar to that used in reverse phase high performance liquid chromatograph technology. The continuous flow reactor 10 is compatible with high performance liquid chromatography technology and Edman and Stark chemistry technology. The discrete objects 20 in the continuous flow reactor 10 provide for good mass transfer characteristics which are clearly superior to the characteristic in existing cartridge technology.
Figure 5 shows chromatograms which provide comparisons of sequencing results, obtained by using sperm whale apomyoglobin, between a cartridge reaction chamber as shown in Hawke, et al., su~ra, and a continuous flow reactor 10 of this invention.
Specifically, figure 5 shows comparative sequencing results obtained in cycle 1 through cycle 4, and the results obtained in cycles 7, 9, 10 and 12.
The upper panels A-H in Figure 5 show selected Edman degradation cycles for the sequencing of 200 picomoles of sperm whale apomyoglobin. The sample was sequenced using a cartridge reaction chamber made from polytetrafluoroethylene as described in ~he manuscript by Hawke et al (1985) cited above. Before the sample could be applied to the glass fiber disk in the cartridge reaction chamber, it was necessary to coat the glass fiber disk with Polybrene (1 mg) and precycle the disk for two cycles of Edman chemistry. Since the time required for one cycle of Edman chemistry (removal of one amino acid derivative) is about 45 minutes, the precycling adds gO minutes to the analysis time.
; The amino acid derivatives obtained from the cartridge ~ reaction chamber were analyzed by reverse phase high performance~

2~i06 chromatography by a method similar to the method described in thl , above cited Hawke et al (1985).
The lower panels, A'-~' in Figure 5 are the chromatograms obtained from an 80 picomole run of sperm whale apo~yoglobin using a continuous flow reactor 10 as described in this patent.
The continuous flow reactor 10 is connected to the same sequencing apparatus and analyzeA in an identical way at the sam~
attenuation settings as described above for the cartridge reaction chamber of the prior art.
The large offscale peaks labeled DEA and DPTU in the panels of Figure S are common background peaks observed in Edman chemistry. The DEA peak is the phenylthiocarbamyl derivative of diethylamine (DEA). DEA is a trace contaminant of triethylamine (~EAl used as a base in Edman chemistry. The DPTU peak is diphenylthiourea, which is formed from the reaction of phenylisothiocyanate (PITC) with aniline. Aniline is in turn formed from the base catalyzed destruction of PITC.
The peaks described in the previous paragraph plus a number of smaller, unidentified peaks, constitute the background noise which interferes with the identification of the phenylthiohydantoin (PTH) amino acid derivatives. In each cycle, the single letter labeled peak corresponds to the correct assignment: ~J - valine, L - leucine, S - serine (S' - a breakdown product of serine), E - glutamic acid, W - tryptophan, and H - histidine. The peak labeled ~std" is an internal standard (the PTH derivative of aminoisobutyric acid). The peaks labeled in parentheses in the panels are the carryover signals from the previous cycle. Its appearance on a chromatogram is normal.
Even though less than ~0% of the amount of sperm whale apomyoglobin was sequenced on the continuous flow reactor 10, there is adequate sensitivity compared to the results obtained 1.

l~Z~06 with the cartridge reaction chamber. This is seen, for example, by comparing the signals for valine ~V) in panels A and A' or the signals for leucine (L) in panels ~ and B'. Beyond the substantial sensitivity provided by the continuous flow reactor 10 of the present invention there is also an increased signal-to-noise ration improvement provided by the continuous flow reactor 10. The improved signal-to-noise ratios can be directly observed by, for example, comparing the relationships of the signal magnitudes for DEA, V and DPTU in panels A and A'. In panel A the magnitudes of signals for DEA and DPTU, which constitute background noise signals, are greater than that for V, the sought-after assignment. This relationship of signal magnitudes are reversed in panel A' where the results using the continuous flow reactor 10 are shown. Such improved signal-to-noise ratios are repeated in all of the panels.
The continuous flow reactor 10 of this invention considerably improved the capability of the sequencing apparatus to sequence reduced amounts of sample. In addition, the sample was directly analyzed after the addition of Polybrene. No precycling was required.
This represents a savings in the time required before sample analysis can be started.
The above discussion and related illustrations of the present invention are directed primarily to preferred embodiments and practices of the invention.
However, it is believed that numerous changes and modifications in the actual implementation of the concepts described herein will be apparent to those skilled in the art, and it is contemplated that such changes and modifications may be made without departing from the scope of the invention as defined by the following claims.
.

Claims

1. A continuous flow reactor including a first tube for passing reactive fluids and solvents from a peptide sequenator into a reaction chamber packed with peptide coated discrete objects and a second tube for removal of solvents and reaction products from the reaction chamber which comprises:
(A) a reaction chamber formed from a pliable, chemically inert tube;
(B) first and second pliable, chemically inert tubes for connecting the reaction chamber to a sequenator, (C) the inside and outside diameters of said reaction chamber tube and said first and second connecting tubes being so dimensioned that two leak-tight interference fit joints are provided by inserting one end section of a tube into the end section of another tube, one of said leak-tight interference fit joints being provided between said first tube and said reaction chamber and the other being provided between said second tube and said reaction chamber.

2. A continuous flow reactor as defined in claim 1 in which the reaction chamber tube and each of the first and second connecting tubes are formed fro,n fluorocarbon polymer.

3. A continuous flow reactor as defined in claim 1 in which the reaction chamber tube and each of the first and second connecting tubes are formed from polytetrafluoroethylene.

4. The continuous flow reactor of claim 1 in which the discrete peptide coated objects with which the reaction chamber is packed comprise peptide coated porous silica objects.

5. The continuous flow reactor as defined in claim 4 wherein said objects are peptide coated porous silica beads.

6. The continuous flow reactor as defined in Claim 1 in which the reaction chamber tube is provided with a porous support means for the discrete articles with which the chamber is packed.

7. The continuous flow reactor as defined in Claim 1 which the inside and outside diameters of said reaction chamber tube and said first and second connecting tubes are so dimensioned that said first and second connecting tubes are interference fitted inside the reaction chamber tube.

8. The continuous flow reactor as defined in Claim 1 in which the inside and outside diameters of the first connecting tube and the reactor chamber tube are so dimensioned that the first connecting tube is interference fitted inside the reaction chamber and in which the inside and outside diameters of the reaction chamber tube and the second connecting tube are so dimensioned that the reaction chamber tube is interference fitted inside the second connecting tube to provide a reaction chamber free of unswept volumes.